Computer vision: object segmentation. Cell Instance Segmentation
Table of contents
In [1]:
# This Python 3 environment comes with many helpful analytics libraries installed
# It is defined by the kaggle/python Docker image: https://github.com/kaggle/docker-python
# For example, here's several helpful packages to load
import numpy as np # linear algebra
import pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)
# Input data files are available in the read-only "../input/" directory
# For example, running this (by clicking run or pressing Shift+Enter) will list all files under the input directory
import os
for dirname, _, filenames in os.walk('/kaggle/input'):
for filename in filenames:
print(os.path.join(dirname, filename))
# You can write up to 20GB to the current directory (/kaggle/working/) that gets preserved as output when you create a version using "Save & Run All"
# You can also write temporary files to /kaggle/temp/, but they won't be saved outside of the current session
/kaggle/input/sartorius-cell-instance-segmentation/sample_submission.csv /kaggle/input/sartorius-cell-instance-segmentation/train.csv /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/shsy5y/livecell_shsy5y_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/shsy5y/livecell_shsy5y_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/shsy5y/livecell_shsy5y_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/skov3/livecell_skov3_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/skov3/livecell_skov3_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/skov3/livecell_skov3_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/bv2/livecell_bv2_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/bv2/livecell_bv2_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/bv2/livecell_bv2_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/bt474/livecell_bt474_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/bt474/livecell_bt474_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/bt474/livecell_bt474_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/a172/livecell_a172_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/a172/livecell_a172_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/a172/livecell_a172_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/huh7/livecell_huh7_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/huh7/livecell_huh7_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/huh7/livecell_huh7_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/skbr3/livecell_skbr3_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/skbr3/livecell_skbr3_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/skbr3/livecell_skbr3_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/mcf7/livecell_mcf7_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/mcf7/livecell_mcf7_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell_single_cells/mcf7/livecell_mcf7_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell/livecell_coco_test.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell/livecell_coco_train.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/annotations/LIVECell/livecell_coco_val.json /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/images/livecell_train_val_images/SHSY5Y/SHSY5Y_Phase_B10_2_03d08h00m_4.tif /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/images/livecell_train_val_images/SHSY5Y/SHSY5Y_Phase_D10_2_03d00h00m_3.tif /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/images/livecell_train_val_images/SHSY5Y/SHSY5Y_Phase_C10_1_01d04h00m_1.tif /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/images/livecell_train_val_images/SHSY5Y/SHSY5Y_Phase_B10_2_01d04h00m_3.tif /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/images/livecell_train_val_images/SHSY5Y/SHSY5Y_Phase_C10_1_01d20h00m_2.tif /kaggle/input/sartorius-cell-instance-segmentation/LIVECell_dataset_2021/images/livecell_train_val_images/SHSY5Y/SHSY5Y_Phase_D10_1_01d08h00m_2.tif 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Importing the required libraries¶
In [2]:
import torch
from torch import nn
from torch import optim
from torch.utils.tensorboard import SummaryWriter
from torch.utils.data import Dataset, DataLoader
from torchvision import transforms
# import torchvision.transforms.functional as TF
import random
import os, shutil
import numpy as np
import pandas as pd
from PIL import Image
from tqdm.auto import tqdm
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import os
from os.path import join
import matplotlib.pyplot as plt
plt.rcParams.update({'font.size': 18})
import cv2
import torch.nn.functional as F
from torch.utils.data import DataLoader, Dataset, sampler
from albumentations import (HorizontalFlip, VerticalFlip, ShiftScaleRotate, Normalize, Resize, Compose, GaussNoise)
from sklearn.model_selection import train_test_split
from sklearn.metrics import accuracy_score, f1_score
In [3]:
data_train = pd.read_csv('../input/sartorius-cell-instance-segmentation/train.csv')
In [4]:
data_train.head(10)
Out[4]:
| id | annotation | width | height | cell_type | plate_time | sample_date | sample_id | elapsed_timedelta | |
|---|---|---|---|---|---|---|---|---|---|
| 0 | 0030fd0e6378 | 118145 6 118849 7 119553 8 120257 8 120961 9 1... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 1 | 0030fd0e6378 | 189036 1 189739 3 190441 6 191144 7 191848 8 1... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 2 | 0030fd0e6378 | 173567 3 174270 5 174974 5 175678 6 176382 7 1... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 3 | 0030fd0e6378 | 196723 4 197427 6 198130 7 198834 8 199538 8 2... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 4 | 0030fd0e6378 | 167818 3 168522 5 169225 7 169928 8 170632 9 1... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 5 | 0030fd0e6378 | 205984 2 206687 4 207391 5 208095 5 208799 6 2... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 6 | 0030fd0e6378 | 203101 2 203805 5 204509 7 205213 10 205917 12... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 7 | 0030fd0e6378 | 191900 2 192604 3 193308 4 194012 5 194717 5 1... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 8 | 0030fd0e6378 | 184848 3 185551 5 186254 7 186958 8 187662 9 1... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
| 9 | 0030fd0e6378 | 165119 1 165822 4 166526 6 167230 9 167935 9 1... | 704 | 520 | shsy5y | 11h30m00s | 2019-06-16 | shsy5y[diff]_E10-4_Vessel-714_Ph_3 | 0 days 11:30:00 |
Visualization of the images¶
In [5]:
def imshow(num_to_show=9):
plt.figure(figsize=(20,20))
for i in range(num_to_show):
plt.subplot(3, 3, i+1)
plt.grid(False)
plt.xticks([])
plt.yticks([])
img = mpimg.imread(f'../input/sartorius-cell-instance-segmentation/train/{data_train.iloc[i,0]}.png')
plt.imshow(img, cmap='cividis')
imshow()
In [6]:
plt.figure(figsize=(20,20))
current_axis = plt.gca()
plt.grid(False)
plt.xticks([])
plt.yticks([])
img=mpimg.imread(f'../input/sartorius-cell-instance-segmentation/train/{data_train.iloc[0,0]}.png')
plt.imshow(img,cmap='bone')
Out[6]:
<matplotlib.image.AxesImage at 0x7fa18c195790>
In [7]:
def decode_rle_mask(rle_mask, shape):
rle_mask = rle_mask.split()
starts, lengths = [np.asarray(x, dtype=int) for x in (rle_mask[0:][::2], rle_mask[1:][::2])]
starts -= 1
ends = starts + lengths
mask = np.zeros((shape[0] * shape[1]), dtype=np.uint8)
for start, end in zip(starts, ends):
mask[start:end] = 1
mask = mask.reshape(shape[0], shape[1])
return mask
In [8]:
def visualize_image(df, image_id):
image_path = df.loc[df['id'] == image_id, 'id'].values[0]
cell_type = df.loc[df['id'] == image_id, 'cell_type'].values[0]
plate_time = df.loc[df['id'] == image_id, 'plate_time'].values[0]
sample_date = df.loc[df['id'] == image_id, 'sample_date'].values[0]
sample_id = df.loc[df['id'] == image_id, 'sample_id'].values[0]
image = cv2.imread(f'../input/sartorius-cell-instance-segmentation/train/{image_path}.png')
image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
fig, axes = plt.subplots(figsize=(20, 20), ncols=2)
fig.tight_layout(pad=5.0)
axes[0].imshow(image, cmap='gray')
masks = []
for mask in df.loc[df['id'] == image_id, 'annotation'].values:
decoded_mask = decode_rle_mask(rle_mask=mask, shape=image.shape)
masks.append(decoded_mask)
mask = np.stack(masks)
mask = np.any(mask == 1, axis=0)
axes[1].imshow(image, cmap='gray')
axes[1].imshow(mask, alpha=0.4)
for i in range(2):
axes[i].set_xlabel('')
axes[i].set_ylabel('')
axes[i].tick_params(axis='x', labelsize=10, pad=10)
axes[i].tick_params(axis='y', labelsize=10, pad=10)
axes[0].set_title(f'{cell_type}', fontsize=10, pad=12)
axes[1].set_title('Segmentation Mask', fontsize=10, pad=12)
plt.show()
plt.close(fig)
In [9]:
select_image_ids = []
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'shsy5y', 'id'].sample(1).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'shsy5y', 'id'].sample(2).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'shsy5y', 'id'].sample(3).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'cort', 'id'].sample(1).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'cort', 'id'].sample(2).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'cort', 'id'].sample(3).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'astro', 'id'].sample(1).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'astro', 'id'].sample(2).to_list()[0])
select_image_ids.append(data_train.loc[data_train['cell_type'] == 'astro', 'id'].sample(3).to_list()[0])
for image_id in select_image_ids:
visualize_image(df=data_train, image_id=image_id)
In [10]:
DATA_PATH = '../input/sartorius-cell-instance-segmentation'
SAMPLE_SUBMISSION = join(DATA_PATH,'train')
TRAIN_CSV = join(DATA_PATH,'train.csv')
TRAIN_PATH = join(DATA_PATH,'train')
TEST_PATH = join(DATA_PATH,'test')
df_train = pd.read_csv(TRAIN_CSV)
print(f'Training Set Shape: {df_train.shape} - {df_train["id"].nunique()} \
Images - Memory Usage: {df_train.memory_usage().sum() / 1024 ** 2:.2f} MB')
Training Set Shape: (73585, 9) - 606 Images - Memory Usage: 5.05 MB
In [11]:
def rle_decode(mask_rle, shape, color=1):
'''
mask_rle: run-length as string formated (start length)
shape: (height,width) of array to return
Returns numpy array, 1 - mask, 0 - background
'''
s = mask_rle.split()
starts, lengths = [np.asarray(x, dtype=int) for x in (s[0:][::2], s[1:][::2])]
starts -= 1
ends = starts + lengths
img = np.zeros(shape[0] * shape[1], dtype=np.float32)
for lo, hi in zip(starts, ends):
img[lo : hi] = color
return img.reshape(shape)
def build_masks(df_train, image_id, input_shape):
height, width = input_shape
labels = df_train[df_train["id"] == image_id]["annotation"].tolist()
mask = np.zeros((height, width))
for label in labels:
mask += rle_decode(label, shape=(height, width))
mask = mask.clip(0, 1)
return np.array(mask)
Dataset class¶
In [12]:
class CellDataset(Dataset):
def __init__(self, df: pd.core.frame.DataFrame, train:bool):
self.IMAGE_RESIZE = (224, 224)
self.RESNET_MEAN = (0.485, 0.456, 0.406)
self.RESNET_STD = (0.229, 0.224, 0.225)
self.df = df
self.base_path = TRAIN_PATH
self.gb = self.df.groupby('id')
self.transforms = Compose([Resize( self.IMAGE_RESIZE[0], self.IMAGE_RESIZE[1]),
Normalize(mean=self.RESNET_MEAN, std= self.RESNET_STD, p=1),
HorizontalFlip(p=0.5),
VerticalFlip(p=0.5)])
# Split train and val set
all_image_ids = np.array(df_train.id.unique())
np.random.seed(42)
iperm = np.random.permutation(len(all_image_ids))
num_train_samples = int(len(all_image_ids) * 0.9)
if train:
self.image_ids = all_image_ids[iperm[:num_train_samples]]
else:
self.image_ids = all_image_ids[iperm[num_train_samples:]]
def __getitem__(self, idx: int) -> dict:
image_id = self.image_ids[idx]
df = self.gb.get_group(image_id)
# Read image
image_path = os.path.join(self.base_path, image_id + ".png")
image = cv2.imread(image_path)
# Create the mask
mask = build_masks(df_train, image_id, input_shape=(520, 704))
mask = (mask >= 1).astype('float32')
augmented = self.transforms(image=image, mask=mask)
image = augmented['image']
mask = augmented['mask']
# print(np.moveaxis(image,0,2).shape)
return np.moveaxis(np.array(image),2,0), mask.reshape((1, self.IMAGE_RESIZE[0], self.IMAGE_RESIZE[1]))
def __len__(self):
return len(self.image_ids)
Data Loaders¶
In [13]:
ds_train = CellDataset(df_train, train=True)
dl_train = DataLoader(ds_train, batch_size=16, num_workers=2, pin_memory=True, shuffle=False)
In [14]:
ds_test = CellDataset(df_train, train=False)
dl_test = DataLoader(ds_test, batch_size=4, num_workers=2, pin_memory=True, shuffle=False)
Visualization of the images and masks¶
In [15]:
# plot simages and mask from dataloader
batch = next(iter(dl_train))
images, masks = batch
print(f"image shape: {images.shape},\nmask shape:{masks.shape},\nbatch len: {len(batch)}")
plt.figure(figsize=(20, 20))
plt.subplot(1, 3, 1)
plt.xticks([])
plt.yticks([])
plt.imshow(images[1][1])
plt.title('Original image')
plt.subplot( 1, 3, 2)
plt.xticks([])
plt.yticks([])
plt.imshow(masks[1][0])
plt.title('Mask')
plt.subplot( 1, 3, 3)
plt.xticks([])
plt.yticks([])
plt.imshow(images[1][1])
plt.imshow(masks[1][0],alpha=0.2)
plt.title('Both')
plt.tight_layout()
plt.show()
image shape: torch.Size([16, 3, 224, 224]), mask shape:torch.Size([16, 1, 224, 224]), batch len: 2
Train the model¶
In [16]:
class DoubleConv(nn.Module):
def __init__(self, in_ch, out_ch):
super(DoubleConv, self).__init__()
self.conv = nn.Sequential(
nn.Conv2d(in_ch, out_ch, kernel_size=3, stride=1, padding=1),
nn.BatchNorm2d(out_ch),
nn.ReLU(inplace=True),
nn.Conv2d(out_ch, out_ch, kernel_size=3, stride=1, padding=1),
nn.BatchNorm2d(out_ch),
nn.ReLU(inplace=True)
)
def forward(self, x):
x = self.conv(x)
return x
In [17]:
class InConv(nn.Module):
def __init__(self, in_ch, out_ch):
super(InConv, self).__init__()
self.conv = DoubleConv(in_ch, out_ch)
def forward(self, x):
x = self.conv(x)
return x
In [18]:
class Down(nn.Module):
def __init__(self, in_ch, out_ch):
super(Down, self).__init__()
self.mpconv = nn.Sequential(
nn.MaxPool2d(2,2),
DoubleConv(in_ch, out_ch)
)
def forward(self, x):
x = self.mpconv(x)
return x
In [19]:
class Up(nn.Module):
def __init__(self, in_ch, out_ch):
super(Up, self).__init__()
self.up = nn.ConvTranspose2d(in_ch // 2, in_ch // 2, kernel_size=2, stride=2)
self.conv = DoubleConv(in_ch, out_ch)
def forward(self, x1, x2):
x1 = self.up(x1)
x = torch.cat([x2, x1], dim=1)
x = self.conv(x)
return x
In [20]:
class OutConv(nn.Module):
def __init__(self, in_ch, out_ch):
super(OutConv, self).__init__()
self.conv = nn.Conv2d(in_ch, out_ch, 1)
self.sigmoid = nn.Sigmoid()
def forward(self, x):
x = self.conv(x)
x = self.sigmoid(x)
return x
In [21]:
class UNet(nn.Module):
def __init__(self, in_channels, num_classes):
super(UNet, self).__init__()
self.inc = InConv(in_channels, 64)
self.down1 = Down(64, 128)
self.down2 = Down(128, 256)
self.down3 = Down(256, 512)
self.down4 = Down(512, 512)
self.up1 = Up(1024, 256)
self.up2 = Up(512, 128)
self.up3 = Up(256, 64)
self.up4 = Up(128, 64)
self.outc = OutConv(64, num_classes)
def forward(self, x):
x1 = self.inc(x)
x2 = self.down1(x1)
x3 = self.down2(x2)
x4 = self.down3(x3)
x5 = self.down4(x4)
x = self.up1(x5, x4)
x = self.up2(x, x3)
x = self.up3(x, x2)
x = self.up4(x, x1)
x = self.outc(x)
return x
In [22]:
device = torch.device('cuda') if torch.cuda.is_available() else torch.device('cpu')
In [23]:
def train_loop(model, optimizer, criterion, train_loader, device=device):
running_loss = 0
model.train()
pbar = tqdm(train_loader, desc='Iterating over train data')
for imgs, masks in pbar:
# pass to device
imgs = imgs.to(device)
masks = masks.to(device)
# forward
out = model(imgs)
loss = criterion(out, masks)
running_loss += loss.item()*imgs.shape[0] # += loss * current batch size
# optimize
optimizer.zero_grad()
loss.backward()
optimizer.step()
running_loss /= len(train_loader.sampler)
return running_loss
In [24]:
def eval_loop(model, criterion, eval_loader, device=device):
running_loss = 0
model.eval()
with torch.no_grad():
accuracy, f1_scores = [], []
pbar = tqdm(eval_loader, desc='Iterating over evaluation data')
for imgs, masks in pbar:
# pass to device
imgs = imgs.to(device)
masks = masks.to(device)
# forward
out = model(imgs)
loss = criterion(out, masks)
running_loss += loss.item()*imgs.shape[0]
# calculate predictions using output
predicted = (out > 0.5).float()
predicted = predicted.view(-1).cpu().numpy()
labels = masks.view(-1).cpu().numpy()
accuracy.append(accuracy_score(labels, predicted))
f1_scores.append(f1_score(labels, predicted))
acc = sum(accuracy)/len(accuracy)
f1 = sum(f1_scores)/len(f1_scores)
running_loss /= len(eval_loader.sampler)
return {
'accuracy':acc,
'f1_macro':f1,
'loss':running_loss}
In [25]:
def train(model, optimizer, criterion, train_loader, valid_loader,
device=device,
num_epochs=30,
valid_loss_min=np.inf,
logdir='logdir'):
tb_writer = SummaryWriter(log_dir=logdir)
for e in range(num_epochs):
# train for epoch
train_loss = train_loop(
model, optimizer, criterion, train_loader, device=device)
# evaluate on validation set
metrics = eval_loop(
model, criterion, valid_loader, device=device
)
# show progress
print_string = f'Epoch: {e+1} '
print_string+= f'TrainLoss: {train_loss:.5f} '
print_string+= f'ValidLoss: {metrics["loss"]:.5f} '
print_string+= f'ACC: {metrics["accuracy"]:.5f} '
print_string+= f'F1: {metrics["f1_macro"]:.3f}'
print(print_string)
# save the model
if metrics["loss"] <= valid_loss_min:
torch.save(model.state_dict(), 'UNet.pt')
valid_loss_min = metrics["loss"]
In [26]:
# set_seed(21)
model = UNet(3, 1).to(device)
optimizer = optim.Adam(model.parameters(), lr=0.01)
criterion = nn.BCELoss()
In [27]:
# train(model, optimizer, criterion, dl_train, dl_test)
In [28]:
# Load the latest model
model.load_state_dict(torch.load('../input/cell-segment-weights/UNet.pt'))
metrics = eval_loop(model, criterion, dl_test)
print('accuracy:', metrics['accuracy'])
print('f1 macro:', metrics['f1_macro'])
print('test loss:', metrics['loss'])
accuracy: 0.9379160355548469 f1 macro: 0.568453203195297 test loss: 0.14072269164636486
Visualisation of predicted masks¶
In [29]:
with torch.no_grad():
outputs = []
ground_trues = []
imgs_test = []
pbar = tqdm(dl_test, desc='Iterating over evaluation data')
for imgs, masks in pbar:
# pass to device
imgs = imgs.to(device)
masks = masks.to(device)
# forward
out = model(imgs)
predicted = (out > 0.5).float()
# print(predicted.shape)
outputs.extend(predicted)
ground_trues.extend(masks)
imgs_test.extend(imgs)
In [30]:
imgs_test[0].shape
Out[30]:
torch.Size([3, 224, 224])
In [31]:
ground_trues[0].shape
Out[31]:
torch.Size([1, 224, 224])
In [32]:
outputs[0].shape
Out[32]:
torch.Size([1, 224, 224])
In [33]:
for i in range(len(imgs_test)):
plt.figure(figsize=(40, 20))
plt.subplot(1, 3, 1)
plt.xticks([])
plt.yticks([])
plt.imshow(imgs_test[i][0].cpu().numpy())
plt.title('Original image')
plt.subplot( 1, 3, 2)
plt.xticks([])
plt.yticks([])
plt.imshow(ground_trues[i][0].cpu().numpy())
plt.title('Mask')
plt.subplot(1, 3, 3)
plt.xticks([])
plt.yticks([])
plt.imshow(outputs[i][0].cpu().numpy())
plt.title('Predicted')
plt.tight_layout()
plt.show()
Make submission¶
In [34]:
def rle_encoding(x):
dots = np.where(x.flatten() == 1)[0]
run_lengths = []
prev = -2
for b in dots:
if (b>prev+1): run_lengths.extend((b + 1, 0))
run_lengths[-1] += 1
prev = b
return ' '.join(map(str, run_lengths))
def remove_overlapping_pixels(mask, other_masks):
for other_mask in other_masks:
if np.sum(np.logical_and(mask, other_mask)) > 0:
mask[np.logical_and(mask, other_mask)] = 0
return mask
In [35]:
id_1 = '7ae19de7bc2a'
id_2 = 'd48ec7815252'
id_3 = 'd8bfd1dafdc4'
image_ids = []
image_ids.append(id_1)
image_ids.append(id_2)
image_ids.append(id_3)
In [36]:
class CellDatasetTest(Dataset):
def __init__(self):
self.IMAGE_RESIZE = (224, 224)
self.RESNET_MEAN = (0.485, 0.456, 0.406)
self.RESNET_STD = (0.229, 0.224, 0.225)
self.base_path = '../input/sartorius-cell-instance-segmentation/test'
self.transforms = Compose([Resize( self.IMAGE_RESIZE[0], self.IMAGE_RESIZE[1]),
Normalize(mean=self.RESNET_MEAN, std= self.RESNET_STD, p=1),
])
# Split train and val set
self.image_ids = np.array(image_ids)
def __getitem__(self, idx: int):
image_id = self.image_ids[idx]
# Read image
image_path = os.path.join(self.base_path, image_id + ".png")
image = cv2.imread(image_path)
augmented = self.transforms(image=image, target=None)
image = augmented['image']
return np.moveaxis(np.array(image),2,0)
def __len__(self):
return len(self.image_ids)
In [37]:
ds_val = CellDatasetTest()
In [38]:
# ds_val.__getitem__(0)
In [39]:
from torchvision.transforms import functional as F
In [40]:
model.eval();
submission = []
pbar = tqdm(ds_val, desc='Iterating over evaluation data')
for im in range(len(image_ids)):
image_id = image_ids[im]
for sample in pbar:
# for in ds_val:
# print(image_ids[im])
img = sample
# print(image_id)
with torch.no_grad():
result = model(imgs.to(device))
previous_masks = []
for i, mask in enumerate(result):
mask = mask.cpu().numpy()
# Keep only highly likely pixels
binary_mask = mask > 0.5
binary_mask = remove_overlapping_pixels(binary_mask, previous_masks)
previous_masks.append(binary_mask)
rle = rle_encoding(binary_mask)
submission.append((image_id, rle))
# im+=1
# Add empty prediction if no RLE was generated for this image
all_images_ids = [image_id for image_id, rle in submission]
if image_id not in all_images_ids:
submission.append((image_id, ""))
In [41]:
# submission
In [42]:
df_sub = pd.DataFrame(submission, columns=['id', 'predicted'])
df_sub.to_csv("submission.csv", index=False)
df_sub
Out[42]:
| id | predicted | |
|---|---|---|
| 0 | 7ae19de7bc2a | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 1 | 7ae19de7bc2a | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 2 | 7ae19de7bc2a | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 3 | d48ec7815252 | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 4 | d48ec7815252 | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 5 | d48ec7815252 | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 6 | d8bfd1dafdc4 | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 7 | d8bfd1dafdc4 | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |
| 8 | d8bfd1dafdc4 | 2795 3 3019 3 3243 4 3467 4 3691 3 3858 2 4080... |